EMD-2339

Helical reconstruction
20.0 Å
EMD-2339
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Deposition: 25/03/2013
Map released: 26/06/2013
Last modified: 17/07/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2339
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 4blf summary report (pdf.gz) Map and 4blf FULL report (pdf.gz)
EMICSS annotations (xml)

Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.

EMD-2339

Helical reconstruction
20.0 Å
EMD-2339
3D View Gallery
Deposition: 25/03/2013
Map released: 26/06/2013
Last modified: 17/07/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Helical reconstruction
Aggregation State: Helical Array
Specimen preparation [1]
Concentration: 1 mg/mL
Details: Protein was mixed with single-stranded DNA
Buffer
pH: 8.0
Details: 50 mM Tris, 500 mM NaCl
Grid
Details: Quantifoil holey carbon
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Instrument: HOMEMADE PLUNGER
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 1.0 µm - 3.2 µm
Nominal magnification: 50000.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at high-magnification (>100,000), Electron beam tilt params: )
Image Recording [1]
Detector category: CCD
Detector model: GENERIC TVIPS
Average electron dose per image: 20 e/Å2
Details: Image data was collected as focal pairs.
Image processing [1]
Details: Particles were picked and preselected using routines of Xmipp, and then reconstruction was carried out using IHRSR.
Final reconstruction
Resolution: 20.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Details:
⌯ Applied Symmetry
ΔΖ: 14.67 Å
ΔΦ: 110.09°
Software [1]
Name Version Details
Bsoft, EMAN, Xmipp, Spider, IHRSR - -
CTF correction
Details:Phase-flipping
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoEM reconstruction of the Agrobacterium T-complex
Details: ::::EMDATABANK.org::::EMD-2339::::
⬡ Geometry
X Y Z
Dimensions 64 64 64
Origin 0 0 0
Spacing 64 64 64
Voxel size 4.32 Å 4.32 Å 4.32 Å
Contour list
Primary Level Source
True 0.008 AUTHOR